[BioC] Limma - Result output - Error - Help

[Gordon K Smyth]

Dear Atul,

You have uses ebayes() when you intended eBayes().

Best wishes
Gordon

> Date: Thu, 04 Apr 2013 19:01:24 -0400
> From: Atul Kakrana <atulkakrana at gmail.com>
> To: "bioconductor at r-project.org" <bioconductor at r-project.org>
> Subject: [BioC] Limma - Result output - Error - Help
> Message-ID: <515E0644.9050304 at gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hello All,
>
> I wrote a script to analyse affymetrix data but its giving an error
> while using the topTable from limma:
>
> Error in array(x, c(length(x), 1L), if (!is.null(names(x)))
> list(names(x),  :
>  'data' must be of a vector type
>
> I checked all the steps that might be causing the error but couldn't
> find out. So, I trimmed my script to minimal basic and it still gives me
> same error.
>
>> mydata <- ReadAffy()
>> esetRMA <- rma(mydata)
> Background correcting
> Normalizing
> Calculating Expression
>> esetRMA
> ExpressionSet (storageMode: lockedEnvironment)
> assayData: 45101 features, 12 samples
>  element names: exprs
> protocolData
>  sampleNames: 00.0A.CEL 00.0B.CEL ... 12.5C.CEL (12 total)
>  varLabels: ScanDate
>  varMetadata: labelDescription
> phenoData
>  sampleNames: 00.0A.CEL 00.0B.CEL ... 12.5C.CEL (12 total)
>  varLabels: sample
>  varMetadata: labelDescription
> featureData: none
> experimentData: use 'experimentData(object)'
> Annotation: mouse4302
>> sampletype <- c('1','1','1','2','2','2','3','3','3','4','4','4')
>> group <-factor(sampletype)
>> design<- model.matrix(~0+group)
>> colnames(design) <- c('WB','Ten','Eleven','Twelve')
>> fit <- lmFit(esetRMA, design)
>> contrast.matrix<-makeContrasts(Ten-WB, levels=design)
>> fit2<- contrasts.fit(fit,contrast.matrix)
>> fit2 <- ebayes(fit2)
>
>> topTable(fit2, adjust = "fdr", number = 50)
> Error in 1:ncol(fit) : argument of length 0
>
>> topTable(fit2,coef = 1, adjust = "fdr", number = 50)
> Error in array(x, c(length(x), 1L), if (!is.null(names(x)))
> list(names(x),  :
>  'data' must be of a vector type
>
>> results <- decideTests(fit2)
> Error in decideTests(fit2) : Need MArrayLM object
>
>
> Could anybody please explain me or point out what I am missing here? Its
> strange that I wrote a similar script for Illumina which works just fine.
>
> AK
>
> -- 
> Atul Kakrana
> Delaware Technology Park
>

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